[BUG?] Issue with merging from another branch after replacing subdirectory with submodule

[Ben Nason <bnason@netflix.com>]

Hi,

In git if you replace a subdirectory with a submodule in one branch,
every successive merge from another branch without that change will
cause a conflict. To reproduce this please see below (DOS batch file).

Is this expected behavior?

Thanks,
Benbuck

:: prep simple repo with subdir
git init repo
pushd repo
echo foo > foo.txt
git add --all
git commit -m "foo"
mkdir sub
echo bar > sub\bar.txt
git add --all
git commit -m "bar"
popd

:: prep simple submodule
git init submod
pushd submod
echo baz2 > baz.txt
git add --all
git commit -m "baz2"
popd

:: in a new branch: delete subdir, replace with submodule
pushd repo
git checkout -b resub
git rm -rf sub
git commit -m "delete subdir"
git submodule add ../submod sub
git submodule update --init
git commit -m "add submod"

:: in old branch: make an unrelated change
git checkout master
git clean -fd
git rs --hard master
echo foo2 > foo.txt
git commit --all -m "foo2"

:: switch back to new branch
git checkout resub
git rs --hard resub
git submodule update --init
pushd sub
git reset --hard master
popd

:: all is good so far, now merge
git merge master
git status
@echo !!!!!! note the above merge conflict !!!!!!
pause
:: resolve the conflict to keep the submodule
git reset sub
git commit --no-edit


:: make another change to old branch
git checkout master
git clean -fd
git rs --hard master
echo foo3 > foo.txt
git commit --all -m "foo3"
git checkout resub
git rs --hard resub
git submodule update --init
pushd sub
git reset --hard master
popd

:: merge again
git merge master
git status
@echo !!!!!! note that the conflict happens on every single merge !!!!!!
pause

popd